For mRNA expression analysis, data from the lung adenocarcinoma patients with RNA-seq and/or sequencing information in the TCGA dataset were extracted from cbioportal.org. Expression levels of the selected genes were also obtained from the dataset reported by Shedden et al. (45) and Chitale et al. (46). Correlation of mRNA expression levels to patient survival in lung adenocarcinoma was done using the KM plotter [kmplot.com; (47)]. Patients were split by median mRNA expression, and analysis was performed using the lung adenocarcinoma dataset irrespective of grade, stage, or previous treatment regimen. For enrichment analysis, data from lung adenocarcinoma patients with sequencing and RNA-seq information in the TCGA dataset were extracted from cbioportal.org. For correlation analysis, data from lung adenocarcinoma patients with RNA-seq information in the TCGA were extracted from cbioportal.org, and Spearman correlation test was applied to analyze the relationship between paired genes.

To identify genes regulated by LKB1 and CRTC2, datasets from RNA-seq and ChIP-seq experiments in A549-LKB1WT and A549-pBabe cells were cross-referenced. Forty-nine protein-coding genes were identified with mRNA expression and CRTC2 binding log2 fold change < −1. Among those 49 genes, we further analyzed for the presence of canonical CRE sites and mRNA expression in a panel of LKB1-mutant and LKB1 wild-type lung adenocarcinoma tumors (TCGA). Six genes were identified as putative LKB1/CRTC2/CREB targets in the lung adenocarcinoma. Pathway enrichment and Gene Ontology analyses of differentially expressed genes in A549 ID1 knockout and ID1 wild-type cells were done using CANCERTOOL (48).

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